Nicholas Loman

2024

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Colquhoun, R., O’Toole, Á., Hill, V., McCrone, J. T., Yu, X., Nicholls, S. M., Poplawski, R., Whalley, T., Groves, N., Ellaby, N., Loman, N., Connor, T. & Rambaut, A., 17 Oct 2024, In: Virus evolution. 10, 1

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Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes

Mirza, J. D., de Oliveira Guimarães, L., Wilkinson, S., Rocha, E. C., Bertanhe, M., Helfstein, V. C., de-Deus, J. T., Claro, I. M., Cumley, N., Quick, J., Faria, N. R., Sabino, E. C., Kirchgatter, K. & Loman, N. J., 19 Jan 2024, In: Microbial Genomics. 10, 1, 001184.

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2023

Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing

Claro, I. M., Ramundo, M. S., Coletti, T. M., da Silva, C. A. M., Valenca, I. N., Candido, D. S., Sales, F. C. S., Manuli, E. R., de Jesus, J. G., de Paula, A., Felix, A. C., Andrade, P. D. S., Pinho, M. C., Souza, W. M., Amorim, M. R., Proenca-Modena, J. L., Kallas, E. G., Levi, J. E., Faria, N. R. & Sabino, E. C. & 2 others, Loman, N. J. & Quick, J., 24 Apr 2023, In: Wellcome Open Research. 6, 22 p., 241.

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2022

COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

The COVID-19 Genomics U. K. (COG-UK) Consortium, Modat, M., Hammers, A., Spector, T. D., Steves, C. J., Sudre, C. H., Ourselin, S. & Duncan, E. L., Dec 2022, In: Scientific Reports. 12, 1, 17 p., 10904.

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1 Citation (Scopus)

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Recurrent SARS-CoV-2 mutations in immunodeficient patients

Wilkinson, S. A. J., Richter, A., Casey, A., Osman, H., Mirza, J. D., Stockton, J., Quick, J., Ratcliffe, L., Sparks, N., Cumley, N., Poplawski, R., Nicholls, S. N., Kele, B., Harris, K., Peacock, T. P. & Loman, N. J., 11 Aug 2022, In: Virus evolution. 8, 2, veac050.

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2021

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Du Plessis, L., Mccrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., Faria, N. R., Jackson, B., Loman, N. J., O’toole, Á., Nicholls, S. M., Parag, K. V., Scher, E., Vasylyeva, T. I., Volz, E. M. & Watts, A. & 8 others, Bogoch, I. I., COVID-19 Genomics UK (COG-UK) Consortium, Aanensen, D. M., Kraemer, M. U. G., Rambaut, A., Pybus, O. G., Beggs, A. (Contributor) & Khan, K. M., 12 Feb 2021, In: Science. 371, 6530, p. 708-712

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Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity

COG-UK Consortium, Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., Rey, S. M., Nicholls, S. M., Colquhoun, R. M., da Silva Filipe, A., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N. & Li, K. & 12 others, Jarrett, R., Pacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., Goodfellow, I., Loman, N. J., Pybus, O. G., Robertson, D. L., Thomson, E. C., Rambaut, A. & Connor, T. R., 7 Jan 2021, In: Cell. 184, 1, p. 64-75.e11 24 p.

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114 Citations (Scopus)

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Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

The COVID-19 Genomics UK (COG-UK) Consortium, Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., Thakur, N., Collier, D. A., Mlcochova, P., Duncan, L. M., Carabelli, A. M., Kenyon, J. C., Lever, A. M., De Marco, A. & Saliba, C. & 9 others, Culap, K., Cameroni, E., Matheson, N. J., Piccoli, L., Corti, D., James, L. C., Robertson, D. L., Bailey, D. & Gupta, R. K., 29 Jun 2021, In: Cell Reports. 35, 13, 24 p., 109292.

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64 Citations (Scopus)

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Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

COVID-19 Genomics UK (COG-UK) Consortium & Beggs, A., 22 Jul 2021, (E-pub ahead of print) In: Science. 373, 6557, p. 889-895

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2020

Post-acute COVID-19 associated with evidence of bystander t-cell activation and a recurring antibiotic-resistant bacterial pneumonia

Gregorova, M., Morse, D., Brignoli, T., Steventon, J., Hamilton, F., Albur, M., Arnold, D., Thomas, M., Halliday, A., Baum, H., Rice, C., Avison, M. B., Davidson, A. D., Santopaolo, M., Oliver, E., Goenka, A., Finn, A., Wooldridge, L., Amulic, B. & Boyton, R. J. & 10 others, Altmann, D. M., Butler, D. K., McMurray, C., Stockton, J., Nicholls, S., Cooper, C., Loman, N., Cox, M. J., Rivino, L. & Massey, R. C., Dec 2020, In: eLife. 9, p. 1-13 13 p., e63430.

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2019

STOP-Colitis pilot trial protocol: a prospective, open-label, randomised pilot study to assess two possible routes of faecal microbiota transplant delivery in patients with ulcerative colitis

Quraishi, M. N., Yalchin, M., Blackwell, C., Segal, J. P., Sharma, N., Hawkey, P., McCune, V., Hart, A., Gaya, D. R., Ives, N., Magill, L., Loi, S., Hewitt, C., Gerasimidis, K., Loman, N., Hansen, R., McMullan, C., Mathers, J., Quince, C. & Crees, N. & 1 others, Iqbal, T., 11 Nov 2019, In: BMJ open. 9, 11, 8 p., e030659.

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5 Citations (Scopus)

185 Downloads (Pure)

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

Nicholls, S. M., Quick, J. C., Tang, S. & Loman, N. J., 1 May 2019, In: GigaScience.

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65 Citations (Scopus)

2018

Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319

Azevedo Antunes, C., Richardson, E. J., Quick, J., Fuentes-utrilla, P., Isom, G. L., Goodall, E. C., Möller, J., Hoskisson, P. A., Mattos-guaraldi, A. L., Cunningham, A. F., Loman, N. J., Sangal, V., Burkovski, A. & Henderson, I. R., 1 Feb 2018, In: Genome Announcements. 6, 5, p. e01566-17 01566-17.

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2 Citations (Scopus)

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Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015

Pini, A., Zomahoun, D., Duraffour, S., Derrough, T., Charles, M., Quick, J., Loman, N., Cowley, L., Leno, M., Ouedraogo, N., Thiam, O., Hernández-Romieu, A., Iko, A., Keita, H., Konate, D., Soumah, A. A., Bouchouar, E., Ileka-Priouzeau, S., Keita, S. & Diallo, B. & 6 others, Cisse, F., Jansa, J., Carroll, M., Günther, S., Severi, E. & Formenty, P., 22 Mar 2018, In: Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin. 23, 12, 17-00140.

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5 Citations (Scopus)

174 Downloads (Pure)

Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H. E., Pedersen, B. S., Rhie, A., Richardson, H., Quinlan, A. R. & Snutch, T. P. & 6 others, Tee, L., Paten, B., Phillippy, A. M., Simpson, J. T., Loman, N. & Loose, M., Apr 2018, In: Nature Biotechnology. 36, 4, p. 338–345 8 p.

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577 Citations (Scopus)

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Towards a genomics-informed, real-time, global pathogen surveillance system

Gardy, J. L. & Loman, N., 1 Jan 2018, In: Nature Reviews Genetics. 19, 1, p. 9-20 12 p.

Research output: Contribution to journal › Review article › peer-review

184 Citations (Scopus)

2017

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., Franco, L. C., Silva, S. P., Wu, C.-H., Raghwani, J., Cauchemez, S., du Plessis, L., Verotti, M. P., de Oliveira, W. K., Carmo, E. H. & Coelho, G. E. & 54 others, Santelli, A. C. F. S., Vinhal, L. C., Henriques, C. M., Simpson, J. T., Loose, M., Andersen, K. G., Grubaugh, N. D., Somasekar, S., Chiu, C. Y., Muñoz-Medina, J. E., Gonzalez-Bonilla, C. R., Arias, C. F., Lewis-Ximenez, L. L., Baylis, S. A., Chieppe, A. O., Aguiar, S. F., Fernandes, C. A., Lemos, P. S., Nascimento, B. L. S., Monteiro, H. A. O., Siqueira, I. C., de Queiroz, M. G., de Souza, T. R., Bezerra, J. F., Lemos, M. R., Pereira, G. F., Loudal, D., Moura, L. C., Dhalia, R., França, R. F., Magalhães, T., Marques, E. T., Jaenisch, T., Wallau, G. L., de Lima, M. C., Nascimento, V., de Cerqueira, E. M., de Lima, M. M., Mascarenhas, D. L., Neto, J. P. M., Levin, A. S., Tozetto-Mendoza, T. R., Fonseca, S. N., Mendes-Correa, M. C., Milagres, F. P., Segurado, A., Holmes, E. C., Rambaut, A., Bedford, T., Nunes, M. R. T., Sabino, E. C., Alcantara, L. C. J., Loman, N. J. & Pybus, O. G., 24 May 2017, In: Nature. 546, 7658, p. 406-410 5 p.

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265 Citations (Scopus)

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First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador

Márquez, S., Carrera, J., Pullan, S. T., Lewandowski, K., Paz, V., Loman, N., Quick, J., Bonsall, D., Powell, R., Thézé, J., Pybus, O. G., Klenerman, P., Eisenberg, J., Coloma, J., Carroll, M. W., Trueba, G. & Logue, C. H., 23 Feb 2017, In: Genome Announcements. 5, 8, e01673-16.

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3 Citations (Scopus)

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Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., Prieto, K., Reyes, D., Bingham, A. M., Paul, L. M., Robles-Sikisaka, R., Oliveira, G., Pronty, D., Barcellona, C. M., Metsky, H. C. & Baniecki, M. L. & 49 others, Barnes, K. G., Chak, B., Freije, C. A., Gladden-Young, A., Gnirke, A., Luo, C., MacInnis, B., Matranga, C. B., Park, D. J., Qu, J., Schaffner, S. F., Tomkins-Tinch, C., West, K. L., Winnicki, S. M., Wohl, S., Yozwiak, N. L., Quick, J., Fauver, J. R., Khan, K., Brent, S. E., Reiner, R. C., Lichtenberger, P. N., Ricciardi, M. J., Bailey, V. K., Watkins, D. I., Cone, M. R., Kopp, E. W., Hogan, K. N., Cannons, A. C., Jean, R., Monaghan, A. J., Garry, R. F., Loman, N. J., Faria, N. R., Porcelli, M. C., Vasquez, C., Nagle, E. R., Cummings, D. A. T., Stanek, D., Rambaut, A., Sanchez-Lockhart, M., Sabeti, P. C., Gillis, L. D., Michael, S. F., Bedford, T., Pybus, O. G., Isern, S., Palacios, G. & Andersen, K. G., 15 Jun 2017, In: Nature. 546, 7658, p. 401-405 5 p.

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173 Citations (Scopus)

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., Burton, D. R., Lewis-Ximenez, L. L., de Jesus, J. G., Giovanetti, M., Hill, S. C., Black, A., Bedford, T., Carroll, M. W., Nunes, M. & Alcantara, L. C. & 8 others, Sabino, E. C., Baylis, S. A., Faria, N. R., Loose, M., Simpson, J. T., Pybus, O. G., Andersen, K. G. & Loman, N. J., 24 May 2017, In: Nature protocols. 12, 6, p. 1261-1276 16 p.

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280 Citations (Scopus)

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Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain

Dunne, K., Chaudhuri, R., Rossiter, A., Beriotto, I., Cunningham, A., Browning, D. F., Squire, D., Cunningham, A., Cole, J., Loman, N. & Henderson, I., Mar 2017, In: Microbial Genomics. 3, 3, p. mgen000106

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20 Citations (Scopus)

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Virus genomes reveal factors that spread and sustained the Ebola epidemic

Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., Park, D. J., Ladner, J. T., Arias, A., Asogun, D., Bielejec, F., Caddy, S. L., Cotten, M., D'Ambrozio, J., Dellicour, S., Di Caro, A., Diclaro, J. W., Duraffour, S., Elmore, M. J. & Fakoli, L. S. & 76 others, Faye, O., Gilbert, M. L., Gevao, S. M., Gire, S., Gladden-Young, A., Gnirke, A., Goba, A., Grant, D. S., Haagmans, B. L., Hiscox, J. A., Jah, U., Kugelman, J. R., Liu, D., Lu, J., Malboeuf, C. M., Mate, S., Matthews, D. A., Matranga, C. B., Meredith, L. W., Qu, J., Quick, J., Pas, S. D., Phan, M. V. T., Pollakis, G., Reusken, C. B., Sanchez-Lockhart, M., Schaffner, S. F., Schieffelin, J. S., Sealfon, R. S., Simon-Loriere, E., Smits, S. L., Stoecker, K., Thorne, L., Tobin, E. A., Vandi, M. A., Watson, S. J., West, K., Whitmer, S., Wiley, M. R., Winnicki, S. M., Wohl, S., Wölfel, R., Yozwiak, N. L., Andersen, K. G., Blyden, S. O., Bolay, F., Carroll, M. W., Dahn, B., Diallo, B., Formenty, P., Fraser, C., Gao, G. F., Garry, R. F., Goodfellow, I., Günther, S., Happi, C. T., Holmes, E. C., Kargbo, B., Keïta, S., Kellam, P., Koopmans, M. P. G., Kuhn, J. H., Loman, N. J., Magassouba, N., Naidoo, D., Nichol, S. T., Nyenswah, T., Palacios, G., Pybus, O. G., Sabeti, P. C., Sall, A., Ströher, U., Wurie, I., Suchard, M. A., Lemey, P. & Rambaut, A., 20 Apr 2017, In: Nature. 544, 7650, p. 309-315 7 p.

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161 Citations (Scopus)

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2016

Ebola virus persistence in breast milk after no reported illness: A likely source of virus transmission from mother to child

Sissoko, D., Keïta, M., Diallo, B., Aliabadi, N., Fitter, D. L., Dahl, B. A., Akoi Bore, J., Raymond Koundouno, F., Singethan, K., Meisel, S., Enkirch, T., Mazzarelli, A., Amburgey, V., Faye, O., Alpha Sall, A., Magassouba, N., Carroll, M. W., Anglaret, X., Malvy, D. & Formenty, P. & 6 others, Bruce Aylward, R., Keïta, S., Harouna Djingarey, M., Loman, N. J., Günther, S. & Duraffour, S., 10 Dec 2016, (E-pub ahead of print) In: Clinical Infectious Diseases.

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52 Citations (Scopus)

178 Downloads (Pure)

Mobile real-time surveillance of Zika virus in Brazil

Faria, N. R., Sabino, E. C., Nunes, M. R. T., Alcantara, L. C. J., Loman, N. J. & Pybus, O. G., 29 Sept 2016, (E-pub ahead of print) In: Genome medicine. 8, 1, p. 97

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92 Citations (Scopus)

177 Downloads (Pure)

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network

Dallman, T., Inns, T., Jombart, T., Ashton, P., Loman, N., Chatt, C., Messelhaeusser, U., Rabsch, W., Simon, S., Nikisins, S., Bernard, H., le Hello, S., Jourdan da-Silva, N., Kornschober, C., Mossong, J., Hawkey, P., de Pinna, E., Grant, K. & Cleary, P., 25 Aug 2016, In: Microbial Genomics. 2, 8, e000070.

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42 Citations (Scopus)

366 Downloads (Pure)

Real-time, portable genome sequencing for Ebola surveillance

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Bore, J. A., Koundouno, R., Dudas, G., Mikhail, A., Ouédraogo, N., Afrough, B., Bah, A., Baum, J. H. J., Becker-Ziaja, B., Boettcher, J. P., Cabeza-Cabrerizo, M., Camino-Sánchez, Á., Carter, L. L. & Doerrbecker, J. & 82 others, Enkirch, T., García-Dorival, I., Hetzelt, N., Hinzmann, J., Holm, T., Kafetzopoulou, L. E., Koropogui, M., Kosgey, A., Kuisma, E., Logue, C. H., Mazzarelli, A., Meisel, S., Mertens, M., Michel, J., Ngabo, D., Nitzsche, K., Pallasch, E., Patrono, L. V., Portmann, J., Repits, J. G., Rickett, N. Y., Sachse, A., Singethan, K., Vitoriano, I., Yemanaberhan, R. L., Zekeng, E. G., Racine, T., Bello, A., Sall, A. A., Faye, O., Faye, O., Magassouba, N., Williams, C. V., Amburgey, V., Winona, L., Davis, E., Gerlach, J., Washington, F., Monteil, V., Jourdain, M., Bererd, M., Camara, A., Somlare, H., Camara, A., Gerard, M., Bado, G., Baillet, B., Delaune, D., Nebie, K. Y., Diarra, A., Savane, Y., Pallawo, R. B., Gutierrez, G. J., Milhano, N., Roger, I., Williams, C. J., Yattara, F., Lewandowski, K., Taylor, J., Rachwal, P., Turner, D. J., Pollakis, G., Hiscox, J. A., Matthews, D. A., O'Shea, M. K., Johnston, A. M., Wilson, D., Hutley, E., Smit, E., Di Caro, A., Wölfel, R., Stoecker, K., Fleischmann, E., Gabriel, M., Weller, S. A., Koivogui, L., Diallo, B., Keïta, S., Rambaut, A., Formenty, P., Günther, S. & Carroll, M. W., 11 Feb 2016, In: Nature. 530, 7589, p. 228-232 5 p.

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614 Citations (Scopus)

Resurgence of Ebola virus disease in guinea linked to a survivor with virus persistence in seminal fluid for more than 500 days

Diallo, B., Sissoko, D., Loman, N. J., Bah, H. A., Bah, H., Worrell, M. C., Conde, L. S., Sacko, R., Mesfin, S., Loua, A., Kalonda, J. K., Erondu, N. A., Dahl, B. A., Handrick, S., Goodfellow, I., Meredith, L. W., Cotten, M., Jah, U., Guetiya Wadoum, R. E. & Rollin, P. & 12 others, Magassouba, N., Malvy, D., Anglaret, X., Carroll, M. W., Aylward, R. B., Djingarey, M. H., Diarra, A., Formenty, P., Keïta, S., Günther, S., Rambaut, A. & Duraffour, S., 15 Nov 2016, In: Clinical Infectious Diseases. 63, 10, p. 1353-1356 4 p.

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110 Citations (Scopus)

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Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

Mcmurray, C. L., Hardy, K. J., Calus, S. T., Loman, N. J. & Hawkey, P. M., 2 Dec 2016, In: Microbiome. 4, 63.

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8 Citations (Scopus)

177 Downloads (Pure)

The effect of DNA extraction methodology on gut microbiota research applications

Gerasimidis, K., Bertz, M., Quince, C., Brunner, K., Bruce, A., Combet, E., Calus, S., Loman, N. & Ijaz, U. Z., 26 Jul 2016, In: BMC Research Notes. 9, 365.

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33 Citations (Scopus)

154 Downloads (Pure)

Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015

Keita, M., Duraffour, S., Loman, N. J., Rambaut, A., Diallo, B., Magassouba, N., Carroll, M. W., Quick, J., Sall, A. A., Glynn, J. R., Formenty, P., Subissi, L. & Faye, O., Dec 2016, In: Emerging infectious diseases. 22, 12, p. 2149-2152 4 p.

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16 Citations (Scopus)

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Voices of biotech

Amit, I., Baker, D., Barker, R., Berger, B., Bertozzi, C., Bhatia, S., Biffi, A., Demichelis, F., Doudna, J., Dowdy, S. F., Endy, D., Helmstaedter, M., Junca, H., June, C., Kamb, S., Khvorova, A., Kim, D.-H., Kim, J.-S., Krishnan, Y. & Lakadamyali, M. & 36 others, Lappalainen, T., Lewin, S., Liao, J., Loman, N., Lundberg, E., Lynd, L., Martin, C., Mellman, I., Miyawaki, A., Mummery, C., Nelson, K., Paz, J., Peralta-Yahya, P., Picotti, P., Polyak, K., Prather, K., Qin, J., Quake, S., Regev, A., Rogers, J. A., Shetty, R., Sommer, M., Stevens, M., Stolovitzky, G., Takahashi, M., Tang, F., Teichmann, S., Torres-Padilla, M.-E., Tripathi, L., Vemula, P., Verdine, G., Vollmer, F., Wang, J., Ying, J. Y., Zhang, F. & Zhang, T., 10 Mar 2016, In: Nature Biotechnology. 34, 3, p. 270-275 6 p.

Research output: Contribution to journal › Article

4 Citations (Scopus)

2015

A complete bacterial genome assembled de novo using only nanopore sequencing data

Loman, N. J., Quick, J. & Simpson, J. T., Aug 2015, In: Nature Methods. 12, 8, p. 733-5 3 p.

Research output: Contribution to journal › Article › peer-review

476 Citations (Scopus)

Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium

Niebel, M., Quick, J., Prieto, A. M. G., Hill, R. L. R., Pike, R., Huber, D., David, M., Hornsey, M., Wareham, D., Oppenheim, B., Woodford, N., van Schaik, W. & Loman, N., 20 Aug 2015, (E-pub ahead of print) In: International Journal of Antimicrobial Agents.

Research output: Contribution to journal › Article › peer-review

Open Access

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18 Citations (Scopus)

365 Downloads (Pure)

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

Kay, G. L., Sergeant, M. J., Zhou, Z., Chan, J.Z.-M., Millard, A., Quick, J., Szikossy, I., Pap, I., Spigelman, M., Loman, N. J., Achtman, M., Donoghue, H. D. & Pallen, M. J., 7 Apr 2015, In: Nature Communications. 6, 9 p., 6717.

Research output: Contribution to journal › Article › peer-review

Open Access

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92 Citations (Scopus)

164 Downloads (Pure)

Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

Mugumbate, G., Abrahams, K. A., Cox, J. A. G., Papadatos, G., van Westen, G., Lelièvre, J., Calus, S. T., Loman, N. J., Ballell, L., Barros, D., Overington, J. P. & Besra, G. S., 23 Mar 2015, In: PLoS ONE. 10, 3, e0121492.

Research output: Contribution to journal › Article › peer-review

Open Access

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30 Citations (Scopus)

359 Downloads (Pure)

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure

Webber, M. A., Whitehead, R. N., Mount, M., Loman, N., Pallen, M. J. & Piddock, L. J. V., Aug 2015, In: Journal of Antimicrobial Chemotherapy. 70, 8, p. 2241-2248

Research output: Contribution to journal › Article › peer-review

Open Access

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51 Citations (Scopus)

194 Downloads (Pure)

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J., Nair, S., Neal, K., Nye, K., Peters, T., De Pinna, E., Robinson, E., Struthers, K., Webber, M., Catto, A., Dallman, T. J., Hawkey, P. & Loman, N., 30 May 2015, In: Genome Biology. 16, 1, p. 114

Research output: Contribution to journal › Article › peer-review

Open Access

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157 Citations (Scopus)

150 Downloads (Pure)

Real-time digital pathogen surveillance - the time is now

Gardy, J., Loman, N. J. & Rambaut, A., 30 Jul 2015, In: Genome Biology. 16, 3 p., 155.

Research output: Contribution to journal › Comment/debate

Open Access

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63 Citations (Scopus)

133 Downloads (Pure)

Successful test launch for nanopore sequencing

Loman, N. J. & Watson, M., Apr 2015, In: Nature Methods. 12, 4, p. 303-304 2 p.

Research output: Contribution to journal › Article

72 Citations (Scopus)

Twenty years of bacterial genome sequencing

Loman, N. J. & Pallen, M. J., Dec 2015, In: Nature Reviews Microbiology. 13, p. 787-794 8 p.

Research output: Contribution to journal › Article › peer-review

134 Citations (Scopus)

2014

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

Quick, J., Quinlan, A. R. & Loman, N. J., 20 Oct 2014, In: GigaScience. 3, 22.

Research output: Contribution to journal › Article › peer-review

Open Access

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143 Citations (Scopus)

290 Downloads (Pure)

Binning metagenomic contigs by coverage and composition

Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F. & Quince, C., Nov 2014, In: Nature Methods. 11, 11, p. 1144-6 3 p.

Research output: Contribution to journal › Article › peer-review

540 Citations (Scopus)

Biochemical and structural characterization of Mycobacterial aspartyl-tRNA synthetase aspS, a promising TB drug target

Gurcha, S. S., Veeraraghavan, U., Cox, J. A. G., Fütterer, K., Abrahams, K. A., Bhatt, A., Alderwick, L. J., Reynolds, R. C., Loman, N. J., Nataraj, V.-S., Alemparte, C., Barros, D., Lloyd, A. J., Ballell, L., Hobrath, J. V. & Besra, G. S., 19 Nov 2014, In: PLoS ONE. 9, 11, e113568.

Research output: Contribution to journal › Article › peer-review

Open Access

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22 Citations (Scopus)

239 Downloads (Pure)

Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli

Johnson, M. D., Bell, J., Clarke, K., Chandler, R., Pathak, P., Xia, Y., Marshall, R. L., Weinstock, G. M., Loman, N. J., Winn, P. J. & Lund, P. A., 29 Aug 2014, In: Molecular Microbiology. 93, 5, p. 911–927

Research output: Contribution to journal › Article › peer-review

Open Access

File

24 Citations (Scopus)

235 Downloads (Pure)

Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound

Quick, J., Constantinidou, C., Pallen, M. J., Oppenheim, B. & Loman, N. J., 8 May 2014, In: Genome Announcements. 2, 3, e00355-14.

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Poretools: a toolkit for analyzing nanopore sequence data

Loman, N. J. & Quinlan, A. R., 1 Dec 2014, In: Bioinformatics. 30, 23, p. 3399-401 3 p.

Research output: Contribution to journal › Article › peer-review

224 Citations (Scopus)

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

Fothergill, J. L., Neill, D. R., Loman, N., Winstanley, C., Kadioglu, A. & Loman, N., 2014, In: Nature Communications. 5, p. 4780

Research output: Contribution to journal › Article › peer-review

41 Citations (Scopus)

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J. & Walker, A. W., 12 Nov 2014, In: BMC Biology. 12, 87.

Research output: Contribution to journal › Article › peer-review

Open Access

1370 Citations (Scopus)

Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?

Gerasimidis, K., Russell, R., Hansen, R., Quince, C., Loman, N., Bertz, M., Hanske, L., Blaut, M., McGrogan, P., Edwards, C. A. & Loman, N., Jul 2014, In: Inflammatory Bowel Diseases. 20, 7, p. E18-9

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing

Quick, J., Cumley, N., Wearn, C. M., Niebel, M., Constantinidou, C., Thomas, C. M., Pallen, M. J., Moiemen, N. S., Bamford, A., Oppenheim, B. & Loman, N. J., 4 Nov 2014, In: BMJ open. 4, 11, e006278.

Research output: Contribution to journal › Article › peer-review

Open Access

65 Citations (Scopus)

Nicholas Loman

Research output

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